> On 19 May 2026, at 15.25, Kurt Hornik <[email protected]> wrote:
>
>>>>>> Martin Maechler writes:
>
>>>>>> Stephanie Evert
>>>>>> on Sun, 17 May 2026 09:03:52 +0200 writes:
>
>>>> I will revise my feature request to "have an
>>>> easily-discoverable fast p-value-only calculation" for
>>>> those who aren't using the odds ratio or confidence
>>>> interval.
>
>>> fisher.pval() in the "corpora" package.
>
>>> Best, Steph
>
>> Thank you Steph;
>
>> However, I still agree with Chris that it would be nice to have
>> an easy way to basically just get the p-value, in a case where
>> neither the ESTIMATE nor the confidence interval is needed.
>
>> Indeed, I've not unfrequently seen R code snippets
>
>> <some>.test(.........)$p.value
>
>> also in CRAN package R code and I think base R should provide
>> a simple documented way to get only the pvalue in cases where
>> the full test costs a factor of 1000 more, even if is still
>> only microseconds in case of small data sets.
>
>> My svn commit to the R sources, > 22 years ago (!)
>
>> r29551 | maechler | 2004-05-24 21:34 |
>
>> did introduce the optional argument 'conf.int = TRUE' for the
>> 2x2 case _and_ the NEWS entry (of svn rev 29551) has been
>
>>> o fisher.test(*, conf.int=FALSE) allows to skip the confidence interval
>>> computation
>
>> However, Chris is (indirectly) correct -- he did not mention the
>> 'conf.int' option -- but in this very large case, conf.int=FALSE
>> does not help much, as indeed, the unconditionalized
>
>> logdc <- dhyper(support, m, n, k, log = TRUE)
>
>> is already expensive, and also the computation of the sample OR (odds ratio)
>
>> ESTIMATE <- mle(x)
>
>> is costly. Indeed, I will add a new argument to fisher.test() to allow
>> skipping
>> the expensive parts and get the p.value and *still* a valid result
>> of class "htest".
>> For now, this will only be fast when as by default the null
>> hypothesis is `or = 1`
>
> Perhaps we could simply take `or = NULL` or `or = NA` to say "do not
> even estimate the OR"?
>
Hm, no. A simple testonly=TRUE would be better. Double-dutying an argument just
makes it trickier to explain. And you might actually want to get the p-value
for other values of OR.
-p
> -k
>
>> Martin Maechler
>
>> ______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
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--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: [email protected] Priv: [email protected]
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